when I did plasmid purification from TOPO blunt cloned with mCherry insert only, I found that the DNA yield is relatively lower than other clones by 2/3 (its highly reproducible results I don't think its technical problem.).
Anyone experiences this and whats the reasons of this insert could have affected lower yield of DNA in term of biological aspects.
Dear Maccus,
to increase plasmid yield increase the amount of processed culture. That it a simple way ......
You may also need to think to optimize your bacteria (try different strain), growth condition and temperature, ....
I wouldn't be able to explain why it happens, but I can confirm that it's not unusual to have different yields when purifying the same vector with different inserts.
In my hands, some inserts always give me 500ng/ul after a miniprep, while other inserts in the same vector never give me more than 80ng/ul. I suppose that some proteins affect the growth of E.coli or that the plasmid copy number may vary depending on the encoded proteins.
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